bedtools intersect
# input option
-a <A> # Specifies the file "A", which could be in BED/BAM/GFF/VCF format. Each feature in A is compared with B to look for overlaps
-b <B> # Specifies the file "B", which can be one or more BED/BAM/GFF/VCF files. You can pass multiple files or use wildcards (e.g., *.bed)
-abam <A> # Specifically for BAM files used as "A". It compares BAM alignments in A with the features in B
# output option
-ubam # Outputs the BAM file as uncompressed. (Default:compressed BAM)
-bed # When using BAM input for "A", this option outputs the results in BED format. (Default:output remains in BAM format if -abam is used)
-header # Prints the header from the A file before printing the results. Useful for VCF, GFF, or other formats with headers.
-names # When using multiple databases (files in -b), this provides an alias for each file instead of printing a file ID.
-filenames # Similar to -names, but shows the complete filename for each database instead of a file ID.
-sortout # Sorts the output hits from B for each record in A. This can be useful when you're using multiple databases in -b.
# Reporting Options
-wa # Write the original entry in A for each overlap.
-wa # Write the original entry in B for each overlap. (Restricted by -f and -r)
-loj # meaning that each feature in A will be reported with its overlaps in B
-wo # Writes the original entries from both A and B plus the number of base pairs of overlap between them. (Restricted by -f and -r)
-wao # Similar to -wo, but also reports A features with no overlap. (Restricted by -f and -r)
-u # Writes the original entry from A once if any overlap is found with B. (Restricted by -f and -r)
-v # Only reports those entries in A that have no overlap with B. (This is the opposite of -u)
# Counting Options
-c # For each feature in A, reports the number of overlaps found in B. (Restricted -f, -F, -r, and -s)
-C # For each feature in A, it reports the number of overlaps with each B file on separate lines. (Restricted -f, -F, -r, and -s)
# Overlap Requirements
-f # Minimum overlap required as a fraction of A. (Default: is 1E-9 (1bp))
-F # Minimum overlap required as a fraction of B. (Default: 1E-9 (1bp))
-r # Requires reciprocal overlap between A and B, meaning that both must satisfy the minimum overlap fractions.
# For example, if -f is 0.90 and -r is used, this requires that B overlaps at least 90% of A and vice versa.
-e # Requires that the overlap fraction be satisfied for A or B
# In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered.
# Without -e, both fractions would have to be satisfied.
# Strand-Specific(+-链) Options
-s # Enforces "strandedness", meaning that only overlaps on the same strand are considered. (Default: strand is ignored)
-S # Enforces "opposite strandedness", meaning only overlaps on the opposite strand are reported.
# Special Options for BAM Files
-split # Treat “split” BAM (having an “N” CIGAR(Skipped region)operation) or BED12 entries as distinct BED intervals
# performance optimization
-sorted # For very large B files, invokes a "sweeping" algorithm that requires the input to be sorted by chromosome and position
# (e.g., sort -k1,1 -k2,2n).
# This reduces memory usage for large files.
-g <genome file> # pecifies a genome file that defines the expected chromosome order for use with the -sorted option.
-nobuf # Disables buffered output, meaning each line is printed immediately.
# This can slow down large outputs but is useful when output is processed line-by-line.
-iobuf <size> # Sets the size of the read buffer (in bytes).
# Supports suffixes like K, M, or G .
# Currently has no effect with compressed files.
